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courtiol / IsoriX

This is the gthub repository dedicated to the development of the R package IsoriX
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package requiring fix in help links to another package #117

Closed courtiol closed 2 years ago

courtiol commented 3 years ago

Dear All,

This concerns certain help links to other packages in one of the following CRAN packages maintained by you:

EcoGenetics pegas poppr popprxl fakemake pkgbuild LambertW rules workflows FHtest interval IsoriX

For HTML help in R, markup of the form \link[pkg:foo]{topic} in R help pages have traditionally been interpreted as links to the file foo.Rd in package pkg, with fallback to the topic (alias) foo in case the file foo.Rd is not found. R-devel now interprets such markup as links to the topic foo, with fallback to the file foo.Rd if the topic foo does not exist, as this behaviour is more natural (and implicitly assumed by many package authors).

Your package is one of the few on CRAN containing links that change its target help page depending on whether the new or old rules are in effect. This happens because the target package contains both file foo.Rd and topic foo, but in a different file.

Ideally, we would like you to update your package so that the target is unambiguously identified under both rules, so that these links work as intended in both released and development versions of R. For details on how this can be done, please see

https://deepayan.github.io/tmp/topichelp/funs.html

(and the corresponding Rd source at https://github.com/deepayan/misc/blob/master/helptopic/man/funs.Rd).

Kindly submit an update of your package to CRAN as soon as possible fixing these issues. To test your changes, you need a recent version of R-devel, where the new rule is the default, and the old rule can be activated by setting

Sys.setenv("_R_HELP_LINKS_TOTOPICS" = FALSE)

Please let me know if you need any further help.

Regards, -Deepayan

courtiol commented 3 years ago

Could probably be tackled with #93 unless we need to do this soon for CRAN